V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

Urdy, Severine. On the Evolution of Morphogenetic Models: Mechano-Chemical Interactions and an Integrated View of Cell Differentiation, Growth, Pattern Formation and Morphogenesis.. Biological Reviews. Online May, 2012. An extensive article with over 250 references by a University of Zurich post-doctoral researcher that surveys the multiplex course of embryological studies from Immanuel Kant to its 20th century post-DNA stage and onto the current systems biology turn. Often due to instrumentation on hand, along with institute, laboratory, and individual penchants and paradigms, three approaches went forth. A “molecular” school dwelt on how cells differentiate due to morphogen gradients. A “chemical” way focused on spatio-temporal heterogeneties from morphogenetics fields. “Mechanists” were concerned with how three-dimensional shapes arose in cells from physical forces. Today, a promise of synthesis is in the air via a novel bioinformatic engagement that can integrate and understand the role and activity of complex, self-organizing dynamics.

Major differences among these three schools pertain to the concept of self-organization, and models can be classified as morphostatic or morphodynamic. Various examples illustrate the distorted picture that arises from the distinction among differentiation, growth, pattern formation and morphogenesis, based on the idea that the underlying mechanisms are respectively chemical or mechanical. Emerging quantitative approaches integrate the concepts and methods of complex sciences and emphasize the interplay between hierarchical levels of organization via mechano-chemical interactions. They draw upon recent improvements in mathematical and numerical morphogenetic models and upon considerable progress in collecting new quantitative data. This review highlights a variety of such models, which exhibit important advances, such as hybrid, stochastic and multiscale simulations. (Abstract, 1)

Valentine, James. Architectures of Biological Complexity. Integrative and Comparative Biology. 43/1, 2003. A further perception of a nested, iterative genome and subsequent evolution facilitated by scale-free networks.

Van de Vijver, Gertrudis, et al. Reflecting on the Complexity of Biological Systems. Acta Biotheoretica. 51/2, 2003. A lengthy historical survey of evolutionary theory from Immanuel Kant’s "self-organizing" beings to the new science of nonlinear dynamics. Kant’s teleological stratification is now revived in terms of nonequilibrium complex adaptive systems. By these advances a novel, revised path for life’s evolution is achieved which combines a ‘universalist’ source with a ‘constructivist’ context which can converge with the 18th century transcendental vision.

Van de Vijver, Gertrudis, et al, eds. Evolutionary Systems: Biological and Epistemological Perspectives on Selection and Self-Organization.. Dordrecht: Kluwer Academic, 1998. An early example of a genesis synthesis underway as scientists and philosophers begin the necessary marriage of selective and obvious prior generative forces, chance contingency and lawful cause. Various topics are spontaneity, autocatalysis complex dynamics, development, thermodynamic and informational properties along with a semoitic meaning. Vilmos Csanyi, Alicia Juarrero, Michael Conrad, Juan Alvarez de Lorenzana, George Kampis, Stan Salthe, David Depew, Bruce Weber, Robert Riedl, Susantha Goonatilake, Luis Rocha, John Collier, and others bring novel insights. A 2010 paperback edition has since appeared from Springer.

The three well known revolutions of the past centuries - the Copernican, the Darwinian and the Freudian - each in their own way had a deflating and mechanizing effect on the position of humans in nature. They opened up a richness of disillusion: earth acquired a more modest place in the universe, the human body and mind became products of a long material evolutionary history, and human reason, instead of being the central, immaterial, locus of understanding, was admitted into the theater of discourse only as a materialized and frequently out-of-control actor.

The aim of the present book is to elucidate the scientific and philosophical backgrounds that play a role in one of the major debates now taking place in evolutionary thinking, namely that on self-organization and selection. Our focus is therefore on Evolutionary Systems, a field that attempts to address as coherently and as broadly as possible the scientific and epistemological challenges of the concepts of change and evolution. Its main aim is to understand how complex dynamical systems, living and non-living, linguistic or non-linguistic, come to be organized as systems - how, in other words, their inherent dynamical nature gives rise to organizations and forms that have found a balance between potentiality for change and evolution on the one hand, and requisite stability in a given environment on the other. (Preface)

Vane-Wright, Richard. What is Life?: What Might be Said of the Role of Behavior in its Evolution. Biological Journal of the Linnean Society. 112/2, 2014. Carl Linnaeus (1707-1778), the Swedish zoologist founder of biological and ecological taxonomy and nomenclature, would be pleased at a special issue in his name on the many ways that pro-active creatures can influence their own viability and lineage. The emeritus Natural History Museum, London, entomologist here collects authoritative papers from a September 2011 seminar at Burlington House. This introduction, as it ranges widely, is a good synopsis of the state of biological and evolutionary thinking on the verge of an inclusive 21st century synthesis. Sections touch on The Nature of Life on Earth, Can Life be Defined?, to Biotas, Non-Equilibrium Thermodynamics, A Systems View, Self-Organization, Agency, and so on.

Amongst the issue articles are Evolution ‘On Purpose’ by Peter Corning, Between Holism and Reducitonism: A Primer on Emergence, Massimo Pigliucci, Adaptive Evolution without Natural Selection by semiotics scientist Kaveli Kull, and The Role of Behaviour in the Recurrence of Biological Processes by philosopher John Dupre. We post the usual Abstract, an initial caveat (220) that no teleological-like essences have crept in, and some pages on (226) where in their absence, it remains difficult to sort out, or to choose between, a prior self-organization, and life literally winging it as time evolves.

An introduction and overview are provided for a special issue of the Biological Journal of the Linnean Society concerning the role of behaviour in evolution. Conceptual separation of the process of living from the process of evolution has heuristic value, with the potential to ask better questions about both. Following a short account of the origin of this collection of essays, the first main part of the paper assesses current ideas about the nature of living systems. Because all known taxa apparently constitute a single, monophyletic group (superdomain Biota), life can only be characterized, not defined. The second part reviews the ten papers that, collectively, comprise this special issue. It is concluded that we need to acknowledge both the ‘processes of life’ and the ‘processes’ of evolution and we need to explore the consequences that flow from making this distinction. Behaviour, in its broadest sense, is seen as both the expression and mediator of organismic agency, and must therefore play a key role in the processes of evolution. (Abstract)

Whatever the reality, we offer no apologies for this latest attempt to expand or go beyond purely nuclear-genetic, reductionist explanations for adaptive evolution. The search is for non-mystical explanations, fully open to the rigours of normal science. Having edited closely all the papers presented here, I detect no appeal to mystical ‘forces’ or non-material agencies in any of them. (220)

Thus, there is either a central directing agency (e.g. the genome) that results in self organization of life, or organisms have autonomy, bringing about their own maintenance, growth, and reproduction (autopoiesis). Much of what follows in this special issue hinges on this difference, and typically reflects the latter interpretation rather than the former. Organisms are here seen largely as autonomous systems, with agency and a degree of self-determination realized through choice mediated by behavior. (226)

Verd, Berta and Ruben Perez-Carrasco. Interdisciplinary Approaches to Dynamics in Biology. Interface Focus. April, 2021. Oxford University and Imperial College London researchers introduce this current survey of how the complexity sciences, along with better techniques are well along with a 21st century and 2020s global revolution with regard to life’s procreative evolution. Prime papers are Developmental Modules in Metabolism, Cell and Developmental Biology (J. Jaeger, N. Monk) and Process Homology (J. DiFrisco and JJ) (search each). As a synopsis, a recurrent form and function in kind is newly evident for whole organisms (ontogeny), and across creaturely species (phylogeny). In every case and scale, the same network systems are found to be in vivifying effect. This is an historic achievement and discovery in our midst by way of a proposed Charlotte and Charles EarthWin which Natural Genesis seeks to report and document.

It is Time’s Time: Biology is dynamic in nature. From ecological systems to embryonic pattern formation: change is at the centre of any biological phenomenon. The last three decades of molecular genetics have been very successful at identifying the components involved in many biological processes, and we now are at the advent of exciting times where new methodologies and technologies are, for the first time, allowing us to address the dynamics of these processes directly. Life scientists can now quantify the dynamics of biological processes and image them in unprecedented resolution. These and other advances are shifting biological phenomena away from static representations and towards increasingly dynamic and therefore realistic accounts. (First Paragraph)

Vermeij, Geerat. Historical Contingency and the Purported Uniqueness of Evolutionary Innovations. Proceedings of the National Academy of Sciences. 103/1804, 2006. Much local particularity occurs in life’s upward procession but the presence and activity of dynamic self-organization prior to selection serves to guide evolution and history along predictable and repeatable convergent pathways.

Purportedly unique innovations either arose from the union and integration of previously independent components or belong to classes of functionally similar innovations. Claims of singularity are therefore not well supported by the available evidence. Details of initial conditions, evolutionary pathways, phenotypes, and timing are contingent, but important ecological, functional, and directional aspects of the history of life are replicable and predictable. (1804)

Vermeij, Geerat. Nature: An Economic History. Princeton: Princeton University Press, 2004. The distinguished professor of paleoecology at the University of California, Davis achieves a new understanding of biological and social evolution as an inherently economic process. Implicit in this view is the activity of interdependent entities which engage in production, division of labor, consumption, cooperation, shared information, and so on within a larger collective extending from microbes to markets. The same universal principles are noticed to hold at each subsequent stage.

A synthesis of this kind may strike many readers as impossibly ambitious, even presumptuous. My response is that there is now sufficient theory and observation available to warrant such a synthesis, however imperfect it maybe. (xi) If the thesis of this book is correct, economic life on our planet has exhibited a long-term, though occasionally interrupted, trend toward increased power and independence….Human history recapitulates these same trends over a greatly compressed time span. (292)

Vermeij, Geerat. Power, Competition, and the Nature of History. Paleobiology. Online October, 2019. In this capsule essay, the UC Davis biogeologist draws on his many years of steady research which enables him to recognize and define the presence of a central evolutionary course, as the Abstract and quotes explain. It is really evident that this must be the case from microbes to a metropolis, but natural history has often avoided or denied this admission. See also recent writings by Robert Hazen and George McGhee for similar takes.

Historians have debated whether pathways and events from the past to the present are influenced by contingency, the dependence of outcomes on particular prior conditions, or whether there is long-term emergent directional change. Using evidence from the fossil record and the metabolic evolution of organisms, I show here that power (total energy taken up and expended per unit time) has increased stepwise over time at ecosystem and global scales due to the ratchet-like, cumulative effects of competition and cooperation and to the influence of top competitors and opportunistic species. The history of life thus exhibits an emergent directionality at larger ecosystem phases. (Abstract)

Both sides of this debate (chance/course) focus on participants – lineages and clades in the case of evolution – rather than on the processes to which they are subjected. I suggest that that this emphasis on actors rather than interactions is misplaced, and that a reorientation toward interactions and their outcomes resolves and eliminates the apparent conflict between a contingent and a directional view of history. (2)

Finally, the increasing concentration of power over time might characterize all emergent systems and interacting particles. Although the underlying mechanisms proposed here apply to metabolizing organisms, it is an open question whether life is essential for generating directionality. Gravity ensures that larger bodies exert disproportionate influences on their neighborhoods, suggesting a mechanism for concentrating mass and power at large scales to some point defined by black holes. As in the biosphere, contingency reigns at the scale of movements and positions of particles, while interactions among them generate emergent patterns that are more predictably. (12)

Vinicius, Lucio. Modular Evolution. Cambridge: Cambridge University Press, 2010. A University of Cambridge, Leverhulme Centre for Human Evolutionary Studies, postdoctoral fellow joins the overdue project to revise quite inadequate theories of life’s sequential rise from microbe to artifice. This is deftly done within selection, but with a novel inclusion of nature’s recurrent propensity for modular patterns and processes. But it is noted that Charles himself would not now be a Darwinian with its denial of progress. Once again the present work is braced by Maynard-Smith and Szathmary’s nest of “major transitions,” which is gaining broad currency, along with Jablonka and Lamb’s multi-dimension scale. A meld of 19th and 21st century views is thus sought by advising that such a real procession implies an inescapable advance. In further regard, with Conway Morris, the truth that evolution converges on the same form and function over and over can also no longer be ignored. While self-organizing systems are not broached, Erwin Schrodinger’s 1940s physical “Principle of Order from Order” is revived so as to install a more active, informational role for genetic influences, lately seen in force from molecules to verbiage. With Brian Johnson and Sheung Kwan Lam herein, and an increasing cadre, a younger generation of biological theorists strive apace to flesh out this vital, imperative genesis synthesis.

Despite its wide acceptance, the apparent consensus over historical contingency may be unjustified. (18) Convergence conveys the idea that selection has repeatedly driven distinct species to the same evolutionary ends, irrespective of the particularities or historical scars of each lineage: it is therefore a cogent response to the positive constraint argument. (19)

The theory of major transitions has the merit of defining evolutionary increases in complexity both at the phenotypic-organizational (the newly evolved super-units) and genotypic-informational (the new methods of transmitting biological information) levels. (29) Major transitions and the rationale they present for evolutionary increases in complexity suggest that Darwin’s belief in evolutionary progress was not completely unjustified. (29)

Fourth, the gradual origin of new information carriers and their corresponding phenotypes is possible due to the process of modularity transfer. DNA is an efficient carrier of information due to its modular organization consisting of nucleotide units, whose combination gives rise to potentially infinite combinations or sequences. (34) This process has a crucial evolutionary consequence: if proteins are modularly organized like their DNA ‘hard copy,’ they could at least in principle evolve into information carriers themselves. Thus, transcription factors, neural cells and brains, behaviour and cognition, and human language all derived their modular organization from previously existing disposable, modularly organized phenotypic entities. (34)

Finally, it is impossible to ignore an apparent analogy between the transition to human history and the origin of life itself. As seen earlier, life can be equated with the origin of the DNA World, which established a distinction between the first exclusive information carrier (DNA) and the first exclusively functional entities (proteins). Similarly to the autocatalytic ribozymes that transferred its information roles to DNA and functional roles to proteins in the DNA World, thus becoming the mediator and regulator between the two new molecular types, historical humans seem to have evolved into mediators between cultural information predominantly stored in extended information carriers on the one hand, and the production of cultural extended phenotypes on the other: those two processes could be seen as ‘education’ and ‘work’ respectively. (205)

Vujovic, Filip, et al. Cellular Self-Organization: An Overdrive in Cambrian Diversity? BioEssays. July, 2022. University of Sydney system biophysicians contribute another frontier perception of life’s evolutionary motive occasion as more primarily due to these mathematic procreative agencies, rather than post-selection alone. Their certain subject area is this profuse emergence some 540 mys ago. Some sections are Self-Organization: A Decentralized Algorithm to Transform Chaos into Predictability, Self-Organization and Emergence of Morphological Patterns and Emergence of Form and Function in Cellular Self-Organization. Along with 135 references, graphic displays show how this deep drive (natural genesis) provides a formative, organismic effect prior to selection.

See also The Phanerozoic Aftermath of the Cambrian Information Revolution by Shannon Hsieh, et al in Paleobiology, (48/3, 2022) about a concurrent cerebral and cognitive florescence within this expansive era and Self-Organization as a New Paradigm in Evolutionary Biology, Anne Malasse, ed., for a 2022 book-length report of life’s innate creative source.

occupy multiple ecological niches on earth. A variety of explanations have been proposed for this major evolutionary event termed the “Cambrian explosion.” While most address environmental, developmental, and ecological factors, the biological basis for this accelerated species diversity remains largely open. Here we posit that morphogenesis by self-organization enables an uncoupling of the genomic mutational landscape from phenotypic diversification. We thus suggest that accelerated morphological diversification in the Cambrian transition occurred by an activation dormant (reserved) morphological novelties whose molecular underpinnings were seeded in the Precambrian period. (Excerpt)

The basic tenet of the proposed hypothesis is that evolution of metazoan animals with self-organization capacity provided a dormant opportunity for rapid divergence. The same machinery that stabilizes multicellular structure after development, instructs morphogenesis by self-organization during development. Self-organization not only amplifies phenotypic novelties associated with genomic changes but also enables generation of dormant novelties by uncoupling genotype and phenotype. We propose that mutagenesis in the Precambrian era combined with inherent hypermutability of the self-organization lexicon could have contributed to accelerated occupancy of morphospace in transition to the Cambrian period by emergence of dormant novelties as opposed to de novo generation of these novelties. (11)

Wagner, Andreas. Arrival of the Fittest. New York: Current/Penguin, 2014. With a Solving Evolution’s Greatest Puzzle subtitle, this latest work by the University of Zurich evolutionary biologist achieves an overdue 2010s more complete synopsis of how life’s cosmic and earthly development actually went forth. While the legacy of Charles Darwin, natural selection, and the 1950s modern synthesis are noted, an adequate explanatory theory has eluded. The title phrase is from the Dutch geneticist Hugo de Vries (1848-1935) who wrote while selection causes survival of the fittest organisms, it cannot account for their novel appearances. Thus begins a revolutionary contribution with several significant themes.

Evolving life is seen to consistently find uncanny, innovative solutions such as antifreeze proteins, crystalline lenses, or Hox regulatory genes, which features must be inherently possible. As the quotes offer, and increasingly implied today, a deep generative drive must be in constant effect. In collaboration with physicists in Europe and the United States, (AW is also a Santa Fe Institute external professor) regnant organisms and groups are seen as a consequence of a natural, material propensity for spontaneous self-organization from cosmos to civilizations. As other theorists are closing on, a formal claim is made that such a prior, independent, procreative agency is at formative work.

The breakthrough volume goes on to adopt a unique guiding metaphor, beyond machine or computer, which I have not seen so well applied. Drawn from the Argentine essayist Jorge Luis Borges (1899-1986), the whole universe can well be imagined as a vast library-like repository of books which do contain knowledge, but without a systematic arrangement. By this once and future trope, phenomenal people are thus invited to search, decipher, translate and read. And Andreas Wagner then takes the huge step to aver that nature’s textual script must be genetic in kind. Virtual libraries of all metabolisms, protein structures and gene networks are proposed. A confluence is thus accomplished by a leading scientist to (re)join biology and physics to allow and articulate an organic genesis with its own genotype code.

“Natural selection can preserve innovations, but it cannot create them. Nature’s many innovations—some uncannily perfect—call for natural principles that accelerate life’s ability to innovate.” Darwin’s theory of natural selection explains how useful adaptations are preserved over time. Can random mutations over a mere 3.8 billion years really be responsible for wings, eyeballs, knees, camouflage, lactose digestion, photosynthesis, and the rest of nature’s creative marvels? In Arrival of the Fittest, renowned evolutionary biologist Andreas Wagner draws on over fifteen years of research to present the missing piece in Darwin's theory. Using experimental and computational technologies that were heretofore unimagined, he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take. (Publisher)

Self-organization permeates the universe so completely that most of us don’t even notice it. Much older that life and natural selection, self-organization is how stars and solar systems form, how the earth accreted, how it acquires a moon, oceans, and an atmosphere, and how the continents started to shift. Self-organization creates the microscopic symmetry of a snowflake and the raging clouds of a hurricane, the shifting shapes of sand dunes and the timeless beauty of a crystal. We shouldn’t be surprised to find self-organization in life’s precursors, because it is everywhere else too. (57)

The deepest secrets of nature’s creativity reside in libraries just like this: all-encompassing and hyperastronomically large. Only instead of being written in human language, the texts in these libraries are written in the genetic alphabet of DNA and the molecular functions that DNA encodes. (68-69) For all of those billions of years, nature did not need to know what was around the next corner of the library of evolution to proceed. But if we humans want to understand the library, rather than simply to live in it, we need to have some way to grasp where new and meaningful texts are. And we need a catalog that classifies texts, like the Dewey Decimal System, or the Library of Congress Classification. (93)

These similarities among different libraries are mysterious. How could innovability in metabolism, in proteins, and in regulation circuits have the same source, a library full of chemical meaning with a common cataloging system? The answer is held by an invisible hand that guided the world long before life’s origin – self-organization. (168) Genotype networks are yet another example of pervasive self-organization – the same phenomenon that pervades both the living and nonliving worlds, from the formation of galaxies to the assembly of membranes. They exist in the timeless eternal realm of nature’s libraries. But they certainly have a form of organization so complex that we are just beginning to understand it, and this organization arises all by itself. (175-176) At the core of this innovability is the self-organized multidimensional fabric of genotype networks, hidden behind life’s visible splendor, but creating this splendor. (194)

The mathematical perspective of systems biology also allowed us to decipher the staggeringly complex phenotypic meaning of genotypic texts in nature’s libraries, which is crucial to understanding innovability. It led us to identify genotype networks, and to grasp that genotype networks are the common origin of the different kinds of innovations – in metabolism, regulation, and macromolecules – that created life as we know it. (219) More that that, the mathematics of biology allowed us to see that these libraries self-organize with a simple principle, as simple as the gravitation that helps mold diffuse matter into enoumous galaxies. This principle – that organisms are robust, a consequence of the complexity principle that helps them survive in a changing world – brings forth the intricate organization of these vast libraries. (219)

Platonism has the upper hand in this debate, even though Plato himself was unaware of the best argument for it. It is the startling congruence between mathematical theorems and physical reality, encapsulated in a dictum often attributed to Galileo Galilei: “Mathematics is the language in which God wrote the universe.” (220)

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